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Gene expression profiling of human livers during normothermic machine perfusion

GSE263614 Homo sapiens (human) RNA-seq (gene expression) 206 samples Submitted 2024/08/29 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 206 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
206 samples: 206 samples, each with a distinct title — no replicated groupsGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Transcriptomic signatures during normothermic liver machine perfusion correspond with graft quality and predict the early graft functionEBioMedicine · 2024
Summary (written by the submitters)
Normothermic machine perfusion (NMP) has been successfully implemented in clinical routine of liver transplantation over the past years. However, little is known about the mechanisms how NMP impacts on the transcriptome of a human donor liver. We herein examined gene expression profiles in transplanted and non-transplanted livers over NMP time.
Read the full summary ↓
50 livers subjected to NMP were included in this study. 30 were transplanted after a maximum of 20 hours (h) perfusion, while 15 were discarded due to poor performance. Biopsies were collected befor eNP (PRE), 1h, 6h, 12h, 20h of NMP and after reperfusion. Next-generation sequencing was applied in liver biopsies to assess differential gene expression over perfusion time. Perfusate samples were collected regularly to monitor liver function. Comparison in differential gene expression between PRE and 20h NMP showed 415 upregulated and 727 downregulated genes. Most significantly upregulated genes were associated with extra cellular matrix organization, cell growth/differentiation processes and cytokine signaling. A set of genes were identified which were significantly differentially expressed and important for classification of non-transplanted vs transplanted biopsies, especially at 12 and 20h of NMP. A 7-gene-signature showed good separation already at 6H NMP, thereby CD274 (PD-L1) expression was ponted out as most important.
Published in
Transcriptomic signatures during normothermic liver machine perfusion correspond with graft quality and predict the early graft function
Hautz T, Hackl H, Gottschling H et al. · EBioMedicine 2024 · PMID 39299005 · doi:10.1016/j.ebiom.2024.105330
This dataset
Open GSE263614 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE263614_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1098409 and SRA study SRP500638. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39299005) ↗
Study design
206 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 206 sample titles: 206 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

+ 166 more — browse all 206 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.